BMRB Entry 16222

Name: NMR Structure of Aflatoxin Formamidopyrimidine alpha-anomer in duplex DNA
Published: 2009-11-23

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PDB ID: 2kh3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16222
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of Aflatoxin Formamidopyrimidine alpha-anomer in duplex DNA

Deposition date:

2009-03-24

Original release date:

2009-11-23

Authors:

Brown, Kyle

Citation:

Citation: Brown, Kyle; Voehler, Markus; Magee, Shane; Harris, Constance; Harris, Thomas; Stone, Michael. "Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA." J. Am. Chem. Soc. 131, 16096-16107 (2009).
PubMed: 19831353

Assembly members:

Assembly members:
Aflatoxin_B1_Formamidopyrimidine, polymer, 10 residues, 3365.322 Da.
DNA_(5'-D(*DTP*DGP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DG)-3')_, polymer, 10 residues, 3068.066 Da.

Natural source:

Natural source: Common Name: Aspergillus flavus Taxonomy ID: 5059 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Aspergillus flavus

Experimental source:

Experimental source: Production method: purified from the natural source Host organism: Aspergillus flavus

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Aflatoxin_B1_Formamidopyrimidine: CTATXATTCA
DNA_(5'-D(*DTP*DGP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DG)-3')_: TGAATCATAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	220

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Aflatoxin B1 Formamidopyrimidine	1
2	DNA (5'-D(DTPDGPDAPDAPDTPDCPDAPDTPDAPDG)-3')	2

Entities:

Entity 1, Aflatoxin B1 Formamidopyrimidine 10 residues - 3365.322 Da.

1

DC

DT

DA

DT

FAG

DA

DT

DC

DA

Entity 2, DNA (5'-D(*DTP*DGP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DG)-3') 10 residues - 3068.066 Da.

1

DT

DG

DA

DT

DC

DA

DT

DA

DG

Samples:

sample_1: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; THYMIDINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; Aflatoxin B1 Formamidopyrimidine 1 ± 0.2 mM; 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; D2O 100%; Sodium Phosphate 0.02 M; NaCl 0.1 M; NaN3 10 uM; Na2EDTA 50 uM; DNA_(5'-D(*DTP*DGP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DG)-3')_

sample_2: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; THYMIDINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; Aflatoxin B1 Formamidopyrimidine 1 ± 0.2 mM; 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 1 ± 0.2 mM; H2O 90%; D2O 10%; Sodium Phosphate 0.02 M; NaCl 0.1 M; NaN3 10 uM; Na2EDTA 50 uM; DNA_(5'-D(*DTP*DGP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DG)-3')_ 1 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 8.7; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1H-1H COSY	sample_1	isotropic	sample_conditions_1
1H-1H NOESY	sample_2	isotropic	sample_conditions_1
1H-31P COSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - processing

MARDIGRAS, Borgias, B.A. & James, T.L. - restraint generation

CORMA, James T.L. - structure validation

CURVES, Lavery, R. and Sklenar, H - data analysis

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz